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Old 10-03-2014, 07:15 AM   #1
c_ro87
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Location: Buenos Aires

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Default Help with a probably bad variant call

Hello all,

i have a variant from a ION PGM sequencing, called with the ION Torrent variant caller plugin

CHR POS ID REF ALT

chr22 44324726 . T TG
The flow cell evaluator say this is a insertion

GT:AOP:FAO:FDP:FRO:FSAF:FSAR:FSRF:FSRR:GQ:RO:SAF:SAR:SRF:SRR
1/1:5:27:27:27:0:16:11:0:0:11:22:0:5:16:6
You see FSAF = 16, FSAR = 11, FSRF = 0, FSRR = 0, but the observations are

SAF = 0, SAR=5, SRF=16, SRR=6

if i look the alignment in IGV i see the following




i check in dbSNP and in the position 44324727 a well known C/G snp 1KG MAF G=0.284 rs738409

and the T variant at position 44324730 is also known rs738408



So in my opinion is more likely a C/G rs738409 SNP, than a novel insertion, and even more it looks like a strand bias because the observed alternate allele as an insertion is only in the reverse strand.



What's you opinion?

Last edited by c_ro87; 10-03-2014 at 07:51 AM.
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Old 10-03-2014, 08:46 AM   #2
lindenb
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cross posted: https://www.biostars.org/p/114559/
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Old 10-04-2014, 04:46 PM   #3
c_ro87
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Default

how i delette this?
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